#!/usr/bin/perl -w
use strict;

use FindBin;
use lib ("$FindBin::Bin/..", "/net/cpp-group/Leo/bin", "$FindBin::Bin");
use db_parameters;
use ortho_species;
use chromosomes;
use min_max;
use run_cmd;
use calculate_ortholog_type_in_ortholog_sets;
use Data::Dump qw(dump);


use DBI;


print STDERR <<"HEADLINE";
888888888888888888888888888888888888888888888888888888888888888888888

    Update ortholog_types_after_removing_pseudos

		update ortholog_sets, gene_pseudo_stats
		useful after changes to pseudo genes


888888888888888888888888888888888888888888888888888888888888888888888
HEADLINE



#
#	Get gene to transcript map data
#
my $dbh = connect_to_panda();
$dbh->{RaiseError} = 0;
use get_psql_time;
my $start_time = get_psql_time($dbh);

calculate_ortholog_type_in_ortholog_sets($dbh, $curr_protocol_id, 0);



print STDERR "\tCompleted\n";

log_pipeline_stage($dbh, $curr_protocol_id, 39, 'Update ortholog_sets', $start_time);
$dbh->disconnect();
